Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.ISSN 2051-8188 View this blog in Magazine View.

Wednesday, October 24, 2018

Ottawa Ecobiomics hackathon: graph databases and Wikidata

I spent last week in Ottawa at a "Ecobiomics" hackathon organised by Joel Sachs. Essentially we spent a week exploring the application of linked data to various topics in biodiversity, with an emphasis on looking at working examples. Topics covered included:

A report is being written up which will discuss what we got up to in more detail, but one take away for me is the large cognitive burden that still stands in the way of widespread adoption of linked data approaches in biodiversity. Products such as Metaphactory go some way to hiding the complexity, but the overhead of linked data is high, and the benefits are perhaps less than obvious. Update: for more o this see Dan Brickley's comments on "Semantic Web Interest Group now closed".

In this context, the rise of Wikidata is perhaps the most important development. One thing we'd hoped to do but didn't get that far was to set up our own instance of Wikibase to play with (Wikibase is the software that Wikidata runs on). This is actually pretty straightforward to do if you have Docker installed, see this great post in Medium Wikibase for Research Infrastructure — Part 1 by Matt Miller, which I stumbled across after discovering Bob DuCharme's blog post Running and querying my own Wikibase instance. Running Wikibase on your own machine (if you follow the instructions you also get the SPARQL query interface) means that you can play around with a knowledge graph without worrying about messing up Wikidata itself, or having to negotiate with the Wikidata community if you want to add new properties. It looks like a relatively painless way to discover whether knowledge graphs are appropriate for the problem you're trying to solve. I hope to find time to play with Wikibase further in the future.